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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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utilizing PANDA instead of GRNBoost2 #45

Closed kh49 closed 5 years ago

kh49 commented 6 years ago

Is it possible to utilize output from PANDA for the initial GRN links instead of GENIE3 or GRNBoost2? At first glance, the data formats seem fairly similar, but I'm not clear on whether any conversion is required or not.

s-aibar commented 5 years ago

Dear @pophipi,

The input to RcisTarget is a set of co-expressed genes. You can infer those by any other method instead of GENIE3/GRNBoost, and start SCENIC on the "create regulons step" (runSCENIC_2_createRegulons(): https://github.com/aertslab/SCENIC/blob/master/vignettes/detailedStep_2_createRegulons.Rmd). Of course, the final network results will be different... but if you prefer to use PANDA for any reason, you can certainly give it a try.

There is an example of the input format atk: http://scenic.aertslab.org/examples/SCENIC_MouseBrain/int/2.1_tfModules_forMotifEnrichmet.Rds (e.g. co-expression gene sets as a list, including the candidate TF/regulator in the name).